A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations

Finding an appropriate turbulence model for a given flow case usually calls for extensive experimentation with both models and numerical solution methods. This work presents the design and implementation of a flexible, programmable software framework for assisting with numerical experiments in computational turbulence. The framework targets Reynolds-averaged Navier-Stokes models, discretized by finite element methods. The novel implementation makes use of Python and the FEniCS package, the combination of which leads to compact and reusable code, where model- and solver-specific code resemble closely the mathematical formulation of equations and algorithms. The presented ideas and programming techniques are also applicable to other fields that involve systems of nonlinear partial differential equations. We demonstrate the framework in two applications and investigate the impact of various linearizations on the convergence properties of nonlinear solvers for a Reynolds-averaged Navier-Stokes model. © 2011 Elsevier Ltd.

A novel short neurotoxin, cobrotoxin c, from monocellate cobra (Naja kaouthia) venom: isolation and purification, primary and secondary structure determination, and tertiary structure modeling

A novel short neurotoxin, cobrotoxin c (CBT C) was isolated from the venom of monocellate cobra (Naja kaouthia) using a combination of ion-exchange chromatography and FPLC. Its primary structure was determined by Edman degradation. CBT C is composed of 61 amino acid residues. It differs from cobrotoxin b (CBT B) by only two amino acid substitutions, Thr/Ala11 and Arg/Thr56, which are not located on the functionally important regions by sequence similarity. However, the LD50 is 0.08 mg/g to mice, i.e. approximately five-fold higher than for CBT B. Strikingly, a structure-function relationship analysis suggests the existence of a functionally important domain on the outside of Loop III of CBT C. The functionally important basic residues on the outside of Loop III might have a pairwise interaction with alpha subunit, instead of gamma or delta subunits of the nicotinic acetylcholine receptor (nAChR). (C) 2002 Elsevier Science Inc. All rights reserved.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Modular risk modeling and management of water infrastructure disaster incidents

Water supply and wastewater control are critical elements of society's infrastructure. The objective of this study will be to provide a generic risk assessment tool to provide municipalities and the nation as a whole with a quantifiable assessment of their vulnerability to water infrastructure threats. The approach will prioritize countermeasures and identify where research and development is required to further minimize risk. This paper outlines the current context, primary concerns and state-of-the art in critical infrastructure risk management for the water sector and proposes a novel approach to resolve existing questions in the field. The proposed approach is based on a modular framework that derives a quantitative risk index for varied domains of interest. The approach methodology is scaleable and based on formal definitions of event probability and severity. The framework is equally applicable to natural and human-induced hazard types and can be used for analysis of compound risk events.

Improved jet noise modeling using a new time-scale.

To calculate the noise emanating from a turbulent flow using an acoustic analogy knowledge concerning the unsteady characteristics of the turbulence is required. Specifically, the form of the turbulent correlation tensor together with various time and length-scales are needed. However, if a Reynolds Averaged Navier-Stores calculation is used as the starting point then one can only obtain steady characteristics of the flow and it is necessary to model the unsteady behavior in some way. While there has been considerable attention given to the correct way to model the form of the correlation tensor less attention has been given to the underlying physics that dictate the proper choice of time-scale. In this paper the authors recognize that there are several time dependent processes occurring within a turbulent flow and propose a new way of obtaining the time-scale. Isothermal single-stream flow jets with Mach numbers 0.75 and 0.90 have been chosen for the present study. The Mani-Gliebe-Balsa-Khavaran method has been used for prediction of noise at different angles, and there is good agreement between the noise predictions and observations. Furthermore, the new time-scale has an inherent frequency dependency that arises naturally from the underlying physics, thus avoiding supplementary mathematical enhancements needed in previous modeling.

Fem modeling of periodic arrays of multi-walled carbon nanotubes

Multiwalled carbon nanotubes display dielectric properties similar to those of graphite, which can be calculated using the well known Drude-Lorentz model. However, most computational softwares lack the capacity to directly incorporate this model into the simulations. We present the finite element modeling of optical propagation through periodic arrays of multiwalled carbon nanotubes. The dielectric function of nanotubes was incorporated into the model by using polynomial curve fitting technique. The computational analysis revealed interesting metamaterial filtering effects displayed by the highly dense square lattice arrays of carbon nanotubes, having lattice constants of the order few hundred nanometers. The curve fitting results for the dielectric function can also be used for simulating other interesting optical applications based on nanotube arrays.